Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection

Transcription

1 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection NF VALIDATION -certified workflows for pooled or individual food samples for use with: Pathatrix 10-Pooling Salmonella spp. Kit Pathatrix Salmonella spp. Kit Pathatrix Auto Instrument MicroSEQ Salmonella spp. Detection Kit Applied Biosystems 7500 Fast Real-Time PCR System RapidFinder Express Software Catalog Numbers APS500P, APS50, Publication Number MAN Revision C.0 ABI 29/06 11/13; ABI 29/07 11/13 ALTERNATIVE ANALYTICAL METHODS FOR AGRIBUSINESS nf-validation.afnor.org/en For testing of Food and Environmental samples only.

2 The information in this guide is subject to change without notice. DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT. Revision Date Description C.0 24 October 2016 Added instructions for new validated matrices: cocoa and chocolates. Reorganized guidelines for PCR to align with current style and template. Corporate and legal updates. B.0 September 2014 In Capture the Pathatrix beads on page 18, corrected the wash procedure; now includes 1X- PBS wash. A.0 February 2014 New document. Updated corporate trademark and copyright statements. Limited Use Label License No. 492: Environmental Testing, Quality Control/Quality Assurance Testing, Food and Agricultural Testing: Notice to Purchaser: The purchase of this product conveys to the purchaser the limited, non-transferable right to use the purchased amount of the product (a) to perform internal research for the sole benefit of the purchaser; and (b) for environmental testing, quality control/quality assurance testing, food and agricultural testing, including reporting results of purchaser's activities in environmental testing, quality control/quality assurance testing, food and agricultural testing for a fee or other commercial consideration. No other right is hereby granted expressly, by implication, or by estoppel. This product is for environmental testing, quality control/ quality assurance testing, food and agricultural testing and research purposes only. The purchase of this product does not grant the purchaser any additional rights, including (without limitation) the right to transfer or resell the product in any form or the right to use the product as a therapeutic agent or diagnostics test component. For information on obtaining additional rights, please contact outlicensing@thermofisher.com or Out Licensing, Life Technologies Corporation (part of Thermo Fisher Scientific), 5823 Newton Drive, Carlsbad, California Trademarks: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. Brilliance and Oxoid are trademarks of Oxoid Limited. AFNOR and NF VALIDATION are trademarks of Association Française de Normalisation (AFNOR). Stomacher is a registered trademark of Seward Limited, UK. Whirl-pak is a registered trademark of Wheatherby/Nasco, Inc Thermo Fisher Scientific Inc. All rights reserved.

3 Contents CHAPTER 1 Overview... 5 Procedure overview... 6 Required materials... 8 Materials for enrichment of food samples... 8 Materials for immunomagnetic separation... 8 Materials for PCR detection... 9 Materials for selective agar detection CHAPTER 2 Enrich food samples CHAPTER 3 IMS capture of Salmonella spp. with the Pathatrix Kits Workflow Important procedural guidelines Transfer the enriched culture to the Sample Vessel Load and run the sample Unload the sample Capture the Pathatrix beads CHAPTER 4 PCR detection and confirmation testing Prepare a PCR-ready DNA lysate from captured Pathatrix beads PCR with the MicroSEQ Salmonella spp. Detection Kit and RapidFinder Express Software Workflow Important procedural guidelines for PCR Create or edit a run file in RapidFinder Express Software Prepare the assay beads Set up the PCR reactions Load and run the reactions View results and data analysis Retest individual samples after a positive pooled sample Confirmation testing of PCR-positive individual samples Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 3

4 Contents CHAPTER 5 Selective agar detection and confirmation testing Important procedural guidelines Detect Salmonella spp. by selective agar plating Retest individual samples after a positive pooled sample result Confirmation testing of positive individual samples APPENDIX A Troubleshooting General troubleshooting Investigate warning results or failed runs in SDS Software Interpretation of the amplification plot for samples with a Result Warning APPENDIX B NF VALIDATION by AFNOR Certification APPENDIX C Good laboratory practices for PCR and RT-PCR APPENDIX D Safety Chemical safety Biological hazard safety Documentation and support Food Safety support Customer and technical support Limited product warranty References Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

5 1 Overview IMPORTANT! Before using this product, read and understand the information in the Safety appendix in this document. CAUTION! Salmonella spp. is a Biosafety Level 2 (BSL-2) organism [excluding S. Typhi and S. Paratyphi, which are both Biosafety Level 3 (BSL-3)]. Care must be taken when handling samples that may contain salmonellae. Laboratory personnel must be adequately trained to handle pathogens before being permitted to analyze samples for Salmonella spp. Laboratory personnel must wear appropriate protective equipment, which includes but is not limited to: protective eyewear, face shield, clothing/lab coat, and gloves. Waste should be disposed of in compliance with local and national legislation as appropriate. This guide describes the following NF VALIDATION certified workflows for detection of Salmonella spp. in food samples: 1. Enrichment of food samples. 2. Immunomagnetic separation (IMS) and capture of Salmonella spp. using the Pathatrix Auto Instrument and one of the following kits: The Pathatrix 10-Pooling Salmonella spp. Kit (Cat. no. APS500P), for pooled enriched cultures (up to 10 cultures). The Pathatrix Salmonella spp. Kit (Cat. no. APS50), for individual enriched cultures. 3. Detection of Salmonella spp. using one of the following methods: Real-time PCR detection using the MicroSEQ Salmonella spp. Detection Kit and RapidFinder Express Software on the Applied Biosystems 7500 Fast Real-Time PCR Instrument. Direct plating of captured Pathatrix bead-bacteria complexes on selective agar plates. 4. Retesting of individual samples following a positive pooled sample result, using the same detection method as for the pooled samples. 5. Confirmation testing of individual positive samples as described for each detection method. Ensure that all instruments and equipment are properly installed and calibrated. For calibration information, see the documentation that is provided with your instruments. Refer to Appendix B, NF VALIDATION by AFNOR Certification for detailed information about the validated matrices and food categories. Visit thermofisher.com/foodsafety for a list of certified workflows for detection of Salmonella spp. Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 5

6 1 Chapter 1 Overview Procedure overview Procedure overview The procedure is illustrated in Figure 1. A 25-g food sample is homogenized with 225 ml of enrichment media and incubated for hours at 37 C. For pooled samples, a 5-mL aliquot of enriched culture is combined with up to 9 additional 5-mL aliquots of enriched culture of the same matrix type, for a maximum pooled sample volume of 50 ml (see Table 9 in Appendix B, NF VALIDATION by AFNOR Certification ). Pooled enriched cultures are then subjected to a ~15-minute Pathatrix Auto Instrument cycle with anti-salmonella spp. antibody-coated Pathatrix beads, to separate Salmonella spp. from the sample matrix and background flora. The Salmonella-Pathatrix bead complexes are magnetically captured and resuspended in 120 µl of Nuclease-free Water. For PCR detection, 90 µl of the resuspended beads are mixed with 10 µl of Lysis Buffer and subjected to heat lysis at 97 C for 10 minutes. Pathatrix beads are removed from the lysate using a magnetic particle concentrator or magnetic plate. The resulting lysate undergoes PCR using the MicroSEQ Salmonella spp. Detection Kit. For selective agar detection, 10 µl of the (unlysed) resuspended Pathatrix beadbacteria complexes are streaked onto XLD and Oxoid Brilliance Salmonella Agar. Positive pooled samples are retested individually by reprocessing 10-mL samples of stored individual enriched cultures on the Pathatrix Auto Instrument with the APS50 kit, and continuing through the chosen detection procedure. Independent confirmation testing is performed only on positive individual samples, according to the detection method chosen. 6 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

7 Chapter 1 Overview Procedure overview 1 Samples can be individually tested without pooling using the APS50 kit starting from 10 ml of individual enriched culture, following the same detection and confirmation procedures as for pooled samples, according to the detection method chosen. P o o l e d s a m p l e t e s t i n g I n d i v i d u a l s a m p l e t e s t i n g Individual samples (up to 10) Individual sample enrichment Enriched cultures Individual sample Enriched culture Pooling (10 5-mL samples) 5 ml 5 ml 5 ml 5 ml 50-mL pooled sample (1 Pathatrix Test 10-mL individual sample = Positive postenrichment P a t h a t r i x A u t o S y s t e m 1 Pathatrix Test NOTE: retesting of individual samples from a positive pooled sample must use the same detection method as for the pooled sample. Agar plate or Dilute chocolate or cocoa samples 1:6 PCR: 7500 Fast instrument & MicroSEQ pathogen detection kits Retesting after positive pool: 10-mL individual sample For pooled samples If pooled sample is negative, then each sample in the pool is negative. If pooled sample is positive, then individually retest each enriched culture from the pool. Figure 1 Procedure overview Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 7

8 1 Chapter 1 Overview Required materials Required materials Unless otherwise indicated, all materials are available through the Thermo Fisher Microbiology ordering process or through thermofisher.com. MLS: Fisher Scientific (fisherscientific.com) or other major laboratory supplier. Note: Parts may ship separately depending on configuration and storage conditions. Materials for enrichment of food samples Incubator, 37±1 C Item Homogenizer (for example, Stomacher 400 Laboratory Blender) Homogenizer bag, with mesh, 6 9, 24 oz (Whirl-Pak Filter Bag for Homogenizer Blender, or equivalent) Source MLS Thermo Scientific DB5000A, or equivalent Nasco # B01348WA or equivalent Enrichment media appropriate for the sample type: Buffered peptone water (BPW) Brilliant green (CAS ) Ultra-high temperature (UHT) processed skim milk Oxoid CM1049, DB1049, or equivalent Fisher Scientific B422-25, or equivalent Food retail store Materials for immunomagnetic separation Table 1 Pathatrix 10-Pooling Salmonella spp. Kit (Cat. no. APS500P; 50 cartridge runs; 50 pools of 10 samples; 500 samples) Item Quantity or volume Storage Pre-sterilized Sample and Elution Vessel Packs Pre-sterilized Capture Phase Packs Pre-sterilized Flat Cap Lids 50 each [1] Room temperature Anti-Salmonella spp. Antibody-Coated 2.5 ml 5±3 C [3] Paramagnetic Beads [2] [1] The Pathatrix Auto Plastics Kit is also available as Cat. no. ZNACPT. [2] The beads are available separately as Cat. no. ZBSQCAP500. [3] Refer to the product label for the expiration date. [4] Beads that have been subjected to freezing temperatures may be rendered inactive. Do not freeze. [4] 8 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

9 Chapter 1 Overview Required materials 1 Table 2 Pathatrix Salmonella spp. Kit (Cat. no. APS50; 50 cartridge runs; 50 samples) Item Quantity or volume Storage Pre-sterilized Sample and Elution Vessel Packs Pre-sterilized Capture Phase Packs Pre-sterilized Flat Cap Lids 50 each [1] Room temperature Anti-Salmonella spp. Antibody-Coated 2.5 ml 5±3 C [3] Paramagnetic Beads [2] [1] The Pathatrix Auto Plastics Kit is also available as Cat. no. ZNACPT. [2] The beads are available separately as Cat. no. ZBSQCA. [3] Refer to the product label for the expiration date. [4] Beads that have been subjected to freezing temperatures may be rendered inactive. Table 3 Required materials not included in the Pathatrix kits Do not freeze. [4] Item Pathatrix Auto Instrument, including Sample Vessel Holder and Elution Vessel Holder (Optional) Pathatrix Cartridge Rack; holds 5 Cartridges (Optional) Pathatrix Elution Vessel Holder; holds 5 Elution Vessels [1] PBS, 10X, ph 7.4 Dilute 1:10 in molecular biology-grade water (Cat. no. AM9932 or equivalent) prior to use. Nuclease-free Water Source Cat. no. PATHATRIXAUTO Cat. no. ACARTRACK Cat. no. ATUBERACK Cat. no. AM9624 or AM9625 Cat. no. AM9932 [1] Additional Elution Vessel Holders may be purchased; however, an Elution Vessel Holder is included with the Pathatrix Auto Instrument. Materials for PCR detection Table 4 Materials for PCR-ready DNA sample preparation Item Source Heating block, 97±2 C Sterile 1.5-mL microcentrifuge tubes (Optional) 96-well PCR plates and nonoptical film (for processing large numbers of samples) Nuclease-free Water MLS MLS Cat. nos and , or equivalent Cat. no. AM9938 Lysis Buffer, FS Cat. no Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 9

10 1 Chapter 1 Overview Required materials Item Source Magnetic-particle concentrator: DynaMag -2 Magnet (for use with microcentrifuge tubes) Magnetic rack (for use with 96-well plate; for example, Pathatrix Magnetic Plate or Magnetic Stand-96) Cat. no D Cat. no. MAGNETICPLATE or AM10027 Table 5 MicroSEQ Salmonella spp. Detection Kit [96 reactions; Cat. no ] Component Description Amount Cap color Storage MicroSEQ Salmonella spp. Detection Kit Salmonella spp. Assay Beads, 8-tube strips MicroAmp Optical 8-Cap Strips 12 strips (96 tubes) Green (rack) 1 rack 12 strips (96 caps) N/A 5±3 C Protect from light and moisture. [1] Pathogen Detection Negative Control Pathogen Detection Negative Control 1.5 ml Red 5±3 C [1] Excessive exposure to light may affect the fluorescent probes. To protect the beads from moisture, do not remove the desiccant from the pouch, and seal the pouch tightly each time you remove assay bead strips. Table 6 Required materials not included with the MicroSEQ kit Item Source Instruments and equipment Applied Biosystems 7500 Fast Real-Time PCR Instrument RapidFinder Express Software Version 1.1 or higher 7500 Fast Precision Plate Holder for MicroAmp Tube Strips MicroAmp 96-Well Base Cat. no. A30304 (desktop) Cat. no. A30299 (laptop) Contact your local sales representative. Download the latest version at technical-resources/software-downloads/ rapidfinder-express-software.html Cat. no. A29252 Cat. no. N MicroAmp Cap Installing Tool Cat. no MicroAmp Multi-removal Tool Cat. no Benchtop microcentrifuge with 8-tube strip adapter or Plate centrifuge MLS 10 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

11 Chapter 1 Overview Required materials 1 Item Source Laboratory mixer (Vortex mixer or equivalent) Pipettors: Positive-displacement Air-displacement Multichannel MLS MLS Consumables Aerosol-resistant pipette tips Disposable gloves MLS MLS MicroAmp Fast 8-Tube Strip, 0.1-mL Cat. no MicroAmp Optical 8-Cap Strip, 300 strips Cat. no Reagents Nuclease-Free Water Cat. no. AM9938 Table 7 Materials for confirmation testing of PCR-positive samples Item Source Incubator, 37±1 C Sterile, disposable 10-µL loops Xylose lysine deoxycholate (XLD) agar Oxoid Brilliance Salmonella Agar Oxoid Salmonella Selective Supplement MLS MLS MLS CM1092 SR0194E Materials for additional confirmatory testing of characteristic colonies; see Confirmation testing of PCR-positive individual samples on page 27. Materials for selective agar detection Incubator, 37±1 C Item MLS Source Sterile, disposable 10-µL loops MLS Xylose lysine deoxycholate (XLD) agar MLS Oxoid Brilliance Salmonella Agar CM1092 Oxoid Salmonella Selective Supplement SR0194E Materials for confirmation after selective agar detection, according to the method chosen; see Confirmation testing of positive individual samples on page 29. Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 11

12 2 Enrich food samples Refer to Materials for enrichment of food samples on page 8. For preparation of initial suspensions, follow instructions of EN ISO 6579 and 6887 standards. IMPORTANT! Use proper aseptic technique while handling samples to avoid crosscontamination. 1. Prewarm 225 ml of enrichment media per sample to 37±1 C, as indicated in the following table. Sample type [1] Enrichment media Meat Dairy samples, including milk-derived products Chocolate or cocoa-based samples BPW BPW % Brilliant Green Sterile UHT skim milk % Brilliant Green [1] See Table 9 in Appendix B, NF VALIDATION by AFNOR Certification. 2. Add 225 ml of prewarmed media to 25 g (or 25 ml) of food sample in a homogenizer bag. 3. Process for 1 2 minutes in a homogenizer (Stomacher 400 Laboratory Blender with speed setting Norm, or equivalent). Hand massage foods that cannot be processed in a homogenizer (Narang et al, 2006). 4. Incubate at 37±1 C under static conditions for the time indicated in the following table. Sample type Meat or dairy samples Chocolate or cocoa-based samples Enrichment time Total of hours Total of hours 12 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

13 3 IMS capture of Salmonella spp. with the Pathatrix Kits The Pathatrix Salmonella spp. Kits, when used with the Pathatrix Auto Instrument, permit immunomagnetic separation (IMS) and capture and isolation of Salmonella spp. bacteria from pre-enriched food cultures. The Pathatrix 10-Pooling Salmonella spp. Kit format (Cat. no. APS500P) supports pooling of up to 10 enriched cultures into a single test (total pooled sample volume of 50 ml). The Pathatrix Salmonella spp. Kit (Cat. no. APS50) is also part of the NFvalidated workflow. It can be used to reprocess 10-mL samples of individual enriched cultures after a positive pooled sample result. It can also be used for processing 10-mL samples of individual enriched cultures without pooling. Instructions for processing samples with each kit are provided in this chapter. Refer to Materials for immunomagnetic separation on page 8 for kit contents and other required materials. Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 13

14 3 Chapter 3 IMS capture of Salmonella spp. with the Pathatrix Kits Workflow Workflow Transfer enriched culture to the Sample Vessel (Pool up to 10 samples of enriched cultures at this step) q Load and run the samples q Unload the samples q Capture the Pathatrix beads q Proceed to PCR or selective agar detection Important procedural guidelines Use aseptic technique and good laboratory practices at all times. Take care when handling vessels that contain microorganisms. Avoid generating aerosols, as pathogenic organisms may be present. Dispose of used or unused reagents, used media, sample enrichments, as well as other contaminated disposable materials following procedures for infectious or potentially infectious products. Treat all waste as biohazardous, and handle and dispose of using safe laboratory practices, in accordance and compliance with all appropriate regulations. Transfer the enriched culture to the Sample Vessel 1. Remove the Sample and Elution Vessels from the Pathatrix consumable kit packaging and place into the Sample Vessel Holder (included with the Pathatrix Auto Instrument; see Figure 2). 2. Partially remove the lids from both vessels, making an opening large enough to allow the addition of enriched culture and wash buffer to the vessels. 14 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

15 Chapter 3 IMS capture of Salmonella spp. with the Pathatrix Kits Load and run the sample 3 3. Transfer the enriched culture to the Sample Vessel as indicated in the following table. Pooled sample Sample type Individual enriched culture for retesting after a positive pooled sample Individual enriched culture (no pooling) Procedure Prepare a pooled sample by transferring 5-mL aliquots from up to 10 individually enriched cultures to a Sample Vessel. Note: Pool enriched cultures only from the same matrix type [1]. Transfer 10 ml of stored individual enriched culture, rewarmed for 1 2 hours at 37±1 C, to a Sample Vessel. Transfer 10 ml of enriched culture to a Sample Vessel. [1] Table 9 in Appendix B, NF VALIDATION by AFNOR Certification 4. Store the remaining individual enriched cultures at 5±3 C for potential reanalysis until the test result is confirmed. Note: Do not store enriched cultures for more than 32 hours total. Load and run the sample 1. Add about 35 ml of 1X PBS to the fill line of the Elution Vessel. 2. Replace the lids on the Sample and Elution Vessels, making sure that the vessels are completely sealed. 3. Add 50 µl of the Pathatrix bead suspension from the indicated kit into the spout on the lid of the Sample Vessel (Figure 2). IMPORTANT! Fully resuspend the Pathatrix beads by agitating the bead vial (for example, by vortexing or inversion of sealed bead vial) before adding to the Sample Vessel. Pooled sample Sample type Individual enriched culture for retesting after a positive pooled sample Individual enriched culture (no pooling) Use Pathatrix beads from this kit APS500P APS50 APS50 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 15

16 3 Chapter 3 IMS capture of Salmonella spp. with the Pathatrix Kits Load and run the sample Sample Vessel Spout Sample Vessel Elution Vessel Sterile 1X PBS (35 ml) Sample Vessel Holder (ATUBEHOLD) Figure 2 Add Pathatrix beads to the Sample Vessel 4. Orient the capture phase kit with the valve plunger pointing left and connect the valve firmly to the lids of the Sample and Elution Vessels. Capture Phase Valve Plunger Figure 3 Sample and Elution Vessels assembled with capture phase While handling the assembly, be careful not to rotate, twist, or bend the conical ends of the capture phase, as this may loosen or separate the assembly and create leaks that will affect performance. 5. Holding both vessels, carefully lift the assembled vessels and attached capture phase kit out of the Sample Vessel Holder (Figure 3). 6. Place the vessels into the Cartridge, pushing the vessels firmly in place from the bottom upwards. 7. Firmly push the remainder of the kit into the Cartridge, ensuring that the valve, phase, and syringe are all held securely in the molded recess of the Cartridge (Figure 4). 16 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

17 Chapter 3 IMS capture of Salmonella spp. with the Pathatrix Kits Load and run the sample 3 8. Push the magnet slider across into the locking position and press the magnet release button on the side of the Cartridge to ensure the kit is positioned correctly and the magnets can freely disengage from the phase. IMPORTANT! If the magnet slider is hard to close or does not release cleanly when the release button is pressed, carefully reposition the capture phase and repeat this step. Failure to ensure smooth release will cause magnetic beads to remain captured and reduce overall performance. Syringe Magnet Release Button Phase Sliding Magnet Holder Valve Plunger Sample Vessel Elution Vessel Cartridge Holder (ACARTHOLD) Figure 4 Assembled Cartridge 9. Reset the magnets into the locked position. 10. Insert the Cartridge into the Pathatrix Auto Instrument until it clicks into position. 11. Press the numbered button above the appropriate Cartridge to start the run. The associated LED turns green to indicate the run has started. After ~12 minutes, the LED flashes red and green alternately, prompting the user to unload the sample, as described in the next section. Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 17

18 3 Chapter 3 IMS capture of Salmonella spp. with the Pathatrix Kits Unload the sample Unload the sample 1. Press the button above the appropriate Cartridge to initiate the draining step (approximately 2 minutes). 2. When the draining step is complete and the LED is illuminated red, remove the Cartridge by pulling it out, away from the instrument. 3. Remove the syringe from the Cartridge and carefully pull out the rest of the kit, starting at the top and working downwards. When removing the Sample and Elution Vessels from the Cartridge, hold firmly by the vessels themselves to prevent spillage. 4. Place both vessels with the capture phase attached in the Sample Vessel Holder. 5. Remove the lid from the Elution Vessel to separate it from the rest of the consumable. 6. Leaving the Elution Vessel in the Sample Vessel Holder, lift away and discard the rest of the consumable, including the Sample Vessel. Note: The Elution Vessel contains approximately 200 µl of PBS and Pathatrix beads with the captured bacteria. Capture the Pathatrix beads In this procedure, the Pathatrix beads are magnetically captured and washed using a Sample Vessel Holder (holds 1 Elution Vessel) or an Elution Vessel Holder (holds up to 5 Elution Vessels). Both holders contain magnets to capture beads along one side of the bottom of the Elution Vessels. 1. Leave the Elution Vessel in the Sample Vessel Holder for approximately 1 minute to allow capture of the Pathatrix beads. 2. For chocolate and cocoa-based samples only: after capture of the beads in step 1, pipet the supernatant up and down very gently, to resuspend any cocoa sediment, without disturbing the captured beads. This step optimizes removal of chocolate-matrix residue. 3. While the Elution Vessel is still in the Sample Vessel Holder, carefully remove and discard the PBS from the Elution Vessel, taking care not to disturb the captured Pathatrix beads. 4. Remove the Elution Vessel from the Sample Vessel Holder, add 120 µl of 1X PBS, and pipet up and down to completely resuspend the Pathatrix beads. 5. Place the Elution Vessel in the Sample Vessel Holder and allow it to remain there for approximately 1 minute. 18 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

19 Chapter 3 IMS capture of Salmonella spp. with the Pathatrix Kits Capture the Pathatrix beads 3 6. While the Elution Vessel is still in the Sample Vessel Holder, carefully remove and discard the PBS without disturbing the captured Pathatrix beads. 7. Remove the Elution Vessel from the Sample Vessel Holder and completely resuspend the Pathatrix beads in 120 µl of Nuclease-free Water by pipetting up and down. The Pathatrix bead suspension is ready for detection by real-time PCR (Chapter 4, PCR detection and confirmation testing ) or selective agar plating (Chapter 5, Selective agar detection and confirmation testing ). Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 19

20 4 PCR detection and confirmation testing In this procedure, PCR-ready DNA is prepared from the captured Pathatrix beads, then PCR is performed using the prepared DNA, the MicroSEQ Salmonella spp. Detection Kit and RapidFinder Express Software. Individual samples from PCRpositive pooled samples are retested, and confirmation testing is performed on individual samples. Refer to Materials for PCR detection on page 9 for kit contents and other required materials. Prepare a PCR-ready DNA lysate from captured Pathatrix beads 1. Prefill the appropriate number of 1.5-mL centrifuge tubes or wells of a 96-well PCR plate with 10 µl of Lysis Buffer, FS for all samples being tested, including any needed negative controls. 2. Transfer 90 µl of the resuspended Pathatrix bead pellet to each prefilled tube or well. Note: If you are retesting individual samples after a positive pooled result, concurrently streak 10 µl of the remaining resuspended Pathatrix beads onto selective agar plates for confirmation testing, as described in Retest individual samples after a positive pooled sample on page Incubate sample(s) at 97±2 C for 12±2 minutes in a heating block or thermal cycler. 4. Remove the sample(s) from the heating block or thermal cycler and allow the sample(s) to cool to room temperature (23±5 C) for about 1 minute. 5. Proceed in one of the following ways: Proceed directly to PCR with the MicroSEQ kit, if storage of the DNA samples before PCR is not required. Process further for long-term DNA sample storage as follows: a. Place the DNA samples in a magnetic particle concentrator (if using microcentrifuge tubes) or magnetic plate (if using a 96-well plate). b. Leave the sample in the concentrator for 2±1 minutes. c. Remove up to 60 µl from the top of the sample and add it to a clean microcentrifuge tube or well of a 96-well plate. Avoid the magnetic particle pellet and any lysis debris while removing the DNA sample. 20 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

21 Chapter 4 PCR detection and confirmation testing PCR with the MicroSEQ Salmonella spp. Detection Kit and RapidFinder Express Software 4 d. Store the DNA sample below 18 C for up to 1 year. IMPORTANT! Do not freeze the DNA samples with Pathatrix beads. PCR with the MicroSEQ Salmonella spp. Detection Kit and RapidFinder Express Software MicroSEQ assay beads contain all the components necessary for the real-time PCR: probe and primers for the target of interest, enzyme, and other buffer components. The assay beads also contain an internal positive control (IPC) probe, primers, and template to monitor for PCR inhibition. A Pathogen Detection Negative Control is included in the kit. Unknown samples and positive control samples are provided by the investigator. Workflow Create or edit a run file in RapidFinder Express Software q Prepare the assay beads q Set up the PCR reactions q Load and run the reactions q View results and data analysis Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 21

22 4 Chapter 4 PCR detection and confirmation testing PCR with the MicroSEQ Salmonella spp. Detection Kit and RapidFinder Express Software Important procedural guidelines for PCR Software RapidFinder Express Software determines the Run Layout (plate layout) during creation of the run file, therefore it must be set up before distributing DNA samples to the assay beads. For additional information, refer to the Applied Biosystems RapidFinder Express Software v2.0 Quick Reference (Pub. no ) or the online help within the software. Sample handling Use a new pipette tip for each sample. If you mix the assay beads with the DNA samples by pipetting up and down, keep the pipette tip at the bottom of the tube to minimize aerosol formation and cross-contamination. Follow the recommendations in Appendix C, Good laboratory practices for PCR and RT-PCR. MicroAmp tube strips Follow these instructions to ensure proper storage of the tube strips: Cut the storage pouch at the notch above the resealable strip. Always reseal the storage pouch with desiccant, and replace at 5±3 C. 8-tube strips can be cut apart with scissors. If necessary, trim any remaining connector material from the cut to allow a better fit against adjacent tubes in the 7500 Fast Precision Plate Holder for MicroAmp Tube Strips. MicroAmp Tube Strips are labeled 1 8 on the side of the tubes, to orient tube strips during handling Figure 5 MicroAmp Tube Strip labeling The tube strip is shown with tinted dome caps, as provided in the kit. The dome caps should be replaced the optical cap strips for PCR. If necessary for visual reference from above, mark the tab at one end of the cap strip. Do not mark any of the caps (this could interfere with real-time PCR detection). Seal the tubes with the transparent, optical cap strips provided in the kit. Do not use colored caps or tubes for real-time PCR reactions, because they may affect dye-signal readings during real-time PCR. Always use intact 8-cap strips, even if empty tubes have been added next to reaction tubes. 22 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

23 Chapter 4 PCR detection and confirmation testing PCR with the MicroSEQ Salmonella spp. Detection Kit and RapidFinder Express Software 4 Use the MicroAmp 96-Well Base and the MicroAmp Cap Installing Tool to seal the assay tubes with the optical cap strips. This will avoid collapsing, bending, or misaligning the tubes. Confirm that the strips are straight and that each tube is in line with the adjacent tube. Use a plate adapter for vortexing the tube strips, or hold the strips in the MicroAmp 96-Well Base while vortexing. Create or edit a run file in RapidFinder Express Software Prepare the assay beads The RapidFinder Express Software is designed for use on the Applied Biosystems 7500 Fast Real-Time PCR System and must be set up before aliquoting samples. On the main page of the RapidFinder Express Software, select Create/Edit a Run File, and enter the target pathogen, number of samples, replicates, and positive and negative controls for each target at the prompts. The software determines the sample layout based on the information entered, and creates a run file. Follow the plate layout determined by the RapidFinder Express Software. 1. Transfer the appropriate number of individual tubes or 8-tube strips from the storage pouch to a 96-well base at room temperature (23±5 C). 2. If required by the plate layout, place empty MicroAmp Fast 8-Tube Strips (or partial strips) to balance the tray when the assay tubes are placed in the instrument later. Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 23

24 4 Chapter 4 PCR detection and confirmation testing PCR with the MicroSEQ Salmonella spp. Detection Kit and RapidFinder Express Software Set up the PCR reactions For step-by-step instructions, in RapidFinder Express Software v1.1, select Pipette Samples on the main page. 1. Following the layout determined by RapidFinder Express Software, distribute the DNA sample lysates to MicroSEQ assay beads as described in the following table. DNA sample type Frozen DNA samples (with Pathatrix beads removed and DNA frozen as described in Prepare a PCR-ready DNA lysate from captured Pathatrix beads on page 20) DNA samples that have not been frozen (with Pathatrix beads still present) Procedure 1. Just before use, completely thaw the DNA sample on ice. 2. Before opening, centrifuge briefly to remove condensation from the tubes or plates and avoid cross contamination. 3. Add DNA sample to the MicroSEQ assay bead: For samples from chocolate or cocoa matrices: combine 5 µl of the sample with 25 µl of nuclease-free water, mix, then add to an assay bead. For all other matrices: transfer 30 µl of the sample to an assay bead. 1. Place the DNA samples in a magnetic particle concentrator (if using microcentrifuge tubes) or magnetic plate (if using a 96-well plate). 2. Leave the sample in the concentrator for 2±1 minutes. 3. Add DNA sample to the MicroSEQ assay bead avoiding the magnetic particle pellet and any lysis debris at the bottom of the tube. For samples from chocolate or cocoa matrices: carefully remove 5 µl from the top of the sample and combine with 25 µl of nuclease-free water, mix, then add to an assay bead. For all other matrices: carefully transfer 30 µl from the top of the sample to an assay bead. 4. (Optional) Transfer 30 µl of the remaining sample to a clean microcentrifuge tube, avoiding the magnetic particle pellet and any lysis debris at the bottom of the tube, and store the DNA sample below 18 C for potential reanalysis. 2. Following the layout determined by RapidFinder Express Software, add 30 µl of the Pathogen Detection Negative Control and any positive control samples to the appropriate MicroSEQ assay beads at room temperature (23±5 C), and mix by gently pipetting up and down a few times. Assay beads dissolve in 1 5 seconds. Alternatively, vortex the assay tubes after they are capped, as described in step Cap the tubes, sealing each tube with the transparent optical strip caps provided in the kit. 4. Mark or label one end of the strip cap (but not directly over any one cap) to maintain the strip orientation when transferring the tubes to the instrument tray. 24 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

25 Chapter 4 PCR detection and confirmation testing PCR with the MicroSEQ Salmonella spp. Detection Kit and RapidFinder Express Software 4 5. Make sure that the reactions are thoroughly mixed: if reactions were not previously mixed during the pipetting step, vortex to mix. 6. Make sure that the reagents are at the bottom of tubes: briefly centrifuge the strip tubes at g for about 20 seconds using a centrifuge with a plate adapter or a benchtop microcentrifuge with an 8-strip PCR tube adapter. Load and run the reactions In the RapidFinder Express Software, select Start Instrument Run on the main page, select the appropriate run file, and follow the software prompts. 1. Transfer the tubes to the instrument in the same configuration as the run layout. Use the 7500 Fast Precision Plate Holder for MicroAmp Tube Strips in the instrument. 2. Close the tray to the instrument, and follow the RapidFinder Express Software prompts to start the run. FOR USE WITH 8-STRIP TUBES ONLY Figure Fast instrument tube layout RapidFinder Express Software directs the user to load empty strip tubes in column 1 (far left) and column 12 (far right), if needed. The empty capped 8-tube strips evenly distribute the clamping load applied to the sample tube strips during processing, thereby minimizing the risk of collapsing any tubes. View results and data analysis In the RapidFinder Express Software, select View Results on the main page, select the appropriate run file, and follow the prompts to view results. Data analysis is automated by the software. Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 25

26 4 Chapter 4 PCR detection and confirmation testing Retest individual samples after a positive pooled sample Next steps after viewing results Proceed as indicated in the following table, according to the RapidFinder Express result. Result icon [1] Result Action Positive result Negative result Pooled samples: proceed to Retest individual samples after a positive pooled sample on page 26. Individual samples: proceed to Confirmation testing of PCR-positive individual samples on page 27. No action required. Result warning Dilute 5 µl of the retained DNA sample with 25 µl of Nuclease-free Water and repeat the PCR. [1] RapidFinder Express displays results pictorially. Retest individual samples after a positive pooled sample Pooled samples that test positive by PCR must be retested as individual samples, as follows: 1. Rewarm stored individual enriched cultures at 37±1 C for 1 2 hours. 2. Set up fresh Sample and Elution Vessels in a Sample Vessel Holder, and transfer 10 ml of the warmed individual enriched culture to individual Sample Vessels. 3. Process the individual cultures on the Pathatrix Auto Instrument starting at Load and run the sample on page 15 through Capture the Pathatrix beads on page Follow the procedure Prepare a PCR-ready DNA lysate from captured Pathatrix beads on page 20 with 90 µl of the Pathatrix bead suspension, through PCR with the MicroSEQ Salmonella spp. Detection Kit and RapidFinder Express Software on page Concurrently, streak the remaining unlysed Pathatrix bead suspension onto selective agar for confirmation testing. a. Streak 10 µl (one loopful) of the remaining unlysed Pathatrix bead suspension onto a well-dried XLD agar plate, and streak an additional 10 µl onto Oxoid Brilliance Salmonella Agar. IMPORTANT! We recommend streaking, instead of spreading, to generate isolated colonies. b. Allow the plates to dry for 10 minutes, then invert and incubate at 37±1 C for hours. 26 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

27 Chapter 4 PCR detection and confirmation testing Confirmation testing of PCR-positive individual samples 4 Confirmation testing of PCR-positive individual samples Confirmation testing is performed only on individual samples, not pooled samples. In the context of NF VALIDATION Certification, all individual samples identified as positive by the Pathatrix Auto Salmonella spp. Kit Linked to MicroSEQ Salmonella spp. Detection Kit method must be confirmed by one of the following tests: By using the conventional tests described in the methods standardized by CEN or ISO (including the purification step). The confirmation step must start from the enrichment broth (either BPW or UHT milk). By performing a confirmatory test on observed characteristic colonies from the plated unlysed Pathatrix beads from the individual retested samples ( Retest individual samples after a positive pooled sample on page 26), as described in the following table. Characteristic colonies observed XLD agar Oxoid Brilliance Salmonella Agar No No None required Yes No Biochemical gallery Confirmatory test No Yes Latex test (Oxoid DR1108) Yes Yes Latex test (Oxoid DR1108) on colonies from Oxoid Brilliance Salmonella Agar Using any other method certified by NF VALIDATION ; the principle must be different from that of the Pathatrix Auto Salmonella spp. Kit Linked to MicroSEQ Salmonella spp. Detection Kit method (immunomagnetic separation and PCR). The detection protocol of the second validated method used for the confirmation shall be followed entirely. All steps which are before the step from which the confirmation is started shall be common to both methods (that is, enrichment in BPW at 37 C). In the event of discordant results (positive with the alternative method, nonconfirmed by one of the means described above, and in particular the latex test), the laboratory must follow the necessary steps to ensure the validity of the result obtained. Note: Some strains of Salmonella belonging to the serovar Dublin may show a weak to nil magenta pigmentation, because of their low esterase activity. Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 27

28 5 Selective agar detection and confirmation testing Refer to Materials for selective agar detection on page 11. Important procedural guidelines Wear a facemask when weighing out powders. Take care when boiling agar prior to autoclaving, and wear heat-resistant gloves when handling hot flasks of liquid. Detect Salmonella spp. by selective agar plating Note: We recommend streaking the sample out to generate individual colonies, as opposed to spread plating. 1. Streak 10 µl of the unlysed Pathatrix bead suspension over a well-dried XLD agar plate and another 10 µl onto Oxoid Brilliance Salmonella Agar. 2. Allow the plates to dry for approximately 10 minutes, then invert and incubate at 37±1 C for hours. A presumptive positive result is defined as the isolation of typical, suspicious, or atypical Salmonella spp. colonies on the agar plates used. If a negative result is obtained from a pooled sample, the individual enriched cultures can be discarded, as further testing is not required. If a positive result is obtained from a pooled sample, retest the individual enriched cultures to allow identification of which individual samples in the pool produced the positive result, as described in the next section. Note: Some strains of Salmonella belonging to the serovar Dublin may show a weak to nil magenta pigmentation, because of their low esterase activity. 28 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

29 Chapter 5 Selective agar detection and confirmation testing Retest individual samples after a positive pooled sample result 5 Retest individual samples after a positive pooled sample result Pooled samples that test positive by selective agar must be retested as individual samples, as follows: 1. Rewarm stored individual enriched cultures at 37±1 C for 1 2 hours. 2. Set up fresh Sample and Elution Vessels in a Sample Vessel Holder, and transfer 10 ml of the warmed individual enriched sample to the Sample Vessel. 3. Process the individual samples on the Pathatrix Auto Instrument, starting at Load and run the sample on page 15 through Capture the Pathatrix beads on page Follow the procedure Detect Salmonella spp. by selective agar plating on page 28. A presumptive positive result is defined as the isolation of typical, suspicious, or atypical Salmonella spp. colonies on the agar plates used. 5. Proceed to Confirmation testing of positive individual samples in the next section. Confirmation testing of positive individual samples Confirmation testing is performed only on individual samples, not pooled samples. In the context of NF VALIDATION Certification, all individual samples identified as positive by the Pathatrix Auto Salmonella spp. Kit Linked to Selective Agar Detection method must be confirmed by one of the following tests: By using the conventional tests described in the methods standardized by CEN or ISO (including the purification step). The confirmation step must start from the enrichment broth (either BPW or UHT milk). By performing a confirmatory test on observed characteristic colonies from the plated unlysed Pathatrix beads from the individual retested samples ( Retest individual samples after a positive pooled sample result on page 29), as described in the following table. Characteristic colonies observed XLD agar Oxoid Brilliance Salmonella Agar No No None required Yes No Biochemical gallery Confirmatory test No Yes Latex test (Oxoid DR1108) Yes Yes Latex test (Oxoid DR1108) on colonies from Oxoid Brilliance Salmonella Agar Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 29

30 5 Chapter 5 Selective agar detection and confirmation testing Confirmation testing of positive individual samples Using any other method certified by NF VALIDATION ; the principle must be different from that of the Pathatrix Auto Salmonella spp. Kit Linked to MicroSEQ Salmonella spp. Detection Kit method (immunomagnetic separation and PCR). The detection protocol of the second validated method used for the confirmation shall be followed entirely. All steps which are before the step from which the confirmation is started shall be common to both methods (that is, enrichment in BPW at 37 C). In the event of discordant results (positive with the alternative method, nonconfirmed by one of the means described above, and in particular the latex test), the laboratory must follow the necessary steps to ensure the validity of the result obtained. Note: Some strains of Salmonella belonging to the serovar Dublin may show a weak to nil magenta pigmentation, because of their low esterase activity. 30 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

31 A Troubleshooting General troubleshooting Observation Possible cause Recommended action Enriched culture is curdled. In positive control wells, no IPC signal is detected, but targetspecific signal is detected. In positive control wells, no target-specific signal is detected. In negative control wells, target-specific signal is detected. Samples may be slightly acidic or alkaline (for example, milk powders, fermented milk samples, etc.). A high copy number of target DNA exists in samples, resulting in preferential amplification of the targetspecific DNA. Positive control was omitted (pipetting error). Carryover contamination occurred. Correct the ph of the sample-media mixture before enrichment. 1. Mix the food sample with appropriate enrichment media. 2. Incubate for 60±5 minutes at room temperature (23±5 C). 3. Homogenize the sample and determine the ph. 4. Adjust the ph to 6.8±0.2, and mix well before determining the final ph. Use Pathatrix Foam Filters (Cat. no. PFF) and the Pathatrix 10 Pooling Kit (Cat. no. POOL1010MLN) when sampling curdled enriched cultures. No action is required. The result is considered positive. Repeat the assay. Make sure to pipet the positive control into all positive control wells. 1. Repeat the assay using fresh aliquots of all reagents and clean pipetting equipment. 2. If the negative control continues to show contamination, repeat the assay using a new kit. 3. If the negative control continues to show contamination, contact Technical Support. Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 31

32 A Appendix A Troubleshooting General troubleshooting Observation Possible cause Recommended action In negative control wells, no IPC signal is detected, but a target-specific signal is detected. In unknown wells, no IPC or target-specific signal is detected. In unknown wells, no IPC signal is detected, but target-specific signal is detected. Multicomponent plot signals for FAM, VIC, and ROX detectors increase/decreases during cycles 1 15, but the amplification curve and result are not affected (this observation applies to View in SDS mode). Replicate results for a sample are inconsistent. Carryover contamination caused target signal in negative control wells. Additionally, no IPC signal in negative control wells can be caused by: A high copy number of target DNA exists in samples, resulting in preferential amplification of the target-specific DNA. A problem occurred with IPC amplification. Inhibition of PCR occurred. A high copy number of target DNA exists in samples, resulting in preferential amplification of the targetspecific DNA. Incomplete mixing and dissolution of the lyophilized bead with sample or control. All replicate wells for a sample do not have the same result. To correct carryover contamination, repeat the assay using fresh aliquots of all reagents and clean pipetting equipment. To determine whether IPC amplification is a problem, examine unknown wells for an IPC signal. If an IPC signal is present, IPC amplification is not a problem. Dilute the sample 1:5 with Nuclease-free Water to dilute PCR inhibitors, and repeat the assay. If PCR remains inhibited, repeat the sample preparation. No action is required. The result is considered positive. After addition of 30 µl of sample or Pathogen Negative Control to the bead and capping the tubes: 1. Vortex strips at high speed for about 10 seconds, and centrifuge the strips at g for about 10 seconds. 2. Vortex the strips again on high speed for about 10 seconds, and centrifuge the strips at g for about 1 minute. Ensure that all liquid is at the bottom of the tubes and the beads are fully dissolved before proceeding. If more than two replicates yield the same result (for example, 2 of 3 replicates are negative, but 1 replicate is positive), refer to your laboratory protocol to determine whether to repeat the assay using fresh samples and reagents. If only 2 replicates were run and the results are not consistent, repeat the assay using fresh samples and reagents. 32 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

33 Appendix A Troubleshooting Investigate warning results or failed runs in SDS Software A Observation Possible cause Recommended action Amplicon contamination. Contamination was introduced into the PCR clean area from postamplification reaction tubes that were either opened in the clean area or brought into the PCR clean area from contaminated gloves or solutions. Contamination was introduced into the realtime PCR instrument from crushed and broken PCR reaction tubes. To confirm amplicon contamination, perform the following experiment: Prepare negative control samples using at least one 8-tube strip of MicroSEQ Assay Beads. 1. Divide the assay beads into two sets. a. To the first set of assay beads, add 30 μl of Nuclease-free Water. b. To the second set of assay beads, add 29 μl of Nuclease-free Water plus 1 μl of 1 U/μL Uracil DNA Glycosylase (Cat. no ). 2. Run samples on the 7500 Fast Real-Time PCR Instrument using SDS software and select Fast 7500 run mode. 3. Under the instrument tab: Select Add Step to stage 1 of the PCR cycle that consists of 10 minutes at 50 C. Extend the 95 C step from 20 seconds to 10 minutes. Amplicon contamination is indicated by targetspecific signal in the UNG samples and no target-specific signal in +UNG samples. If the instrument block was contaminated, consult the 7300/7500/7500 Fast Real-Time PCR System Absolute Quantitation Using Standard Curve Getting Started Guide (Pub. no ) and/or contact a service representative to clean the instrument. Investigate warning results or failed runs in SDS Software IMPORTANT! If you modify a RapidFinder Express Software run file in the SDS Software, you cannot open the run file again in the RapidFinder Express Software. To avoid altering a RapidFinder Express Software run file, save the run file under a new name in the SDS Software before performing any actions, as described below. 1. Open the run file in the SDS Software by one of the following methods: From View Results in the RapidFinder Express Software, select and open the run file, then click View in SDS. Open the run file in the SDS Software. 2. Select File4 Save As, then save the run file under a new name. 3. Select the Results tab. Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 33

34 A Appendix A Troubleshooting Investigate warning results or failed runs in SDS Software 4. Select the Amplification Plot tab. 5. Select all locations by clicking the top left corner of the layout. 6. Examine the Amplification Plot in Data mode of Delta Rn vs Cycle (displayed by default). To examine the signal for only tubes of interest, Ctrl + Click the locations below the plot. To examine the signal for only the IPC or a specific target, select the signal of interest from the Detector list at the top right of the plot. Refer to Interpretation of the amplification plot for samples with a Result Warning on page When you finish viewing the run file, exit the SDS software: If you accessed the run file from the RapidFinder Express Software, in the SDS Software, select File4Return to RapidFinder Express Software. If you opened the run file directly in the SDS software, in the SDS Software, select File4Exit. 34 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

35 Appendix A Troubleshooting Interpretation of the amplification plot for samples with a Result Warning A Interpretation of the amplification plot for samples with a Result Warning For the IPC and the pathogen target detector, observe if the curve displayed in the Amplification Plot crosses the highlighted horizontal line, sometimes referred to as the "threshold" line. IMPORTANT! The RapidFinder Express Software will automatically select the appropriate threshold values for each detector. Unless advised by a Thermo Fisher Scientific representative, do not change these values. Additionally, the "highlighted horizontal line," as described above, will appear only when one of the detectors is selected. If "All" detectors are selected, the horizontal line will not be in the correct location for proper visual identification of the sample(s). Observation Possible cause Recommended action IPC curve does not cross the threshold line. IPC and Target curves do not cross the threshold line. IPC curve does cross the threshold line and target curve does not cross the threshold line. IPC in this sample was inhibited. PCR inhibition in the sample. No PCR inhibition. Sample is negative for target detection. Add 5 µl the stored DNA sample lysate to 25 µl of Nuclease-free Water and repeat the PCR. Add 5 µl the stored DNA sample lysate to 25 µl of Nuclease-free Water and repeat the PCR. None needed; result is negative. Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 35

36 B NF VALIDATION by AFNOR Certification Visit thermofisher.com/foodsafety for a list of certified workflows for detection of Salmonella spp. Table 8 NF VALIDATION Certification of the workflow Certification ABI 29/06 11/13; ABI 29/07 11/13 ALTERNATIVE ANALYTICAL METHODS FOR AGRIBUSINESS nf-validation.afnor.org/en Expiration For information about the expiration date of the NF VALIDATION certifications, refer to the certificates, ABI 29/06-11/13 and ABI 29/07-11/13, available at nf-validation.afnor.org/en or at thermofisher.com [1]. [1] In the Product Literature section of the product web page. The following methods have been certified by NF VALIDATION : Pathatrix Auto Salmonella spp. Kit Linked to MicroSEQ Salmonella spp. Detection Kit (Certificate ABI 29/07-11/13) Pathatrix Auto Salmonella spp. Kit Linked to Selective Agar Detection (Certificate ABI 29/06-11/13) The NF VALIDATION study was carried out according to the ISO standard against the reference method detailed in ISO 6579:2002. The validated workflow with PCR detection described in this user guide includes: Enrichment in BPW Pathatrix 10-Pooling Salmonella spp. Kit Pathatrix Salmonella spp. Kit MicroSEQ Salmonella spp. Detection Kit Applied Biosystems 7500 Fast Real-Time PCR Instrument RapidFinder Express Software, Version 1.1 or higher Confirmation testing as described in Confirmation testing of PCR-positive individual samples on page Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

37 Appendix B NF VALIDATION by AFNOR Certification Interpretation of the amplification plot for samples with a Result Warning B Table 9 Validated matrices The validated workflow with selective agar detection described in this user guide includes: Enrichment in BPW Pathatrix 10-Pooling Salmonella spp. Kit Pathatrix Salmonella spp. Kit Selective agar plating on XLD and Oxoid Brilliance Salmonella Agar Confirmation testing as described in Confirmation testing of positive individual samples on page 29 The workflows have been certified for use with the matrices described in the following table. Note: Samples may be pooled only with samples of the same matrix type within a category. Reference method Category Type Example food items EN ISO 6579 (2002): Horizontal method for the detection of Salmonella spp. Heat-treated milk and dairy products Raw beef meats (fresh and frozen, seasoned or not) Sterilized or pasteurized milk and dairy products (UHT, canned or pasteurized) Fermented/acidified milks and yogurts Milks, desserts, ice cream Pasteurized cheeses, creams, butters Dry Milk powders Fresh raw beef meats Frozen raw beef meats Seasoned beef meats Powders for dairy desserts Infant formula with and without probiotic Beef trim and ground beef Beef trim and ground beef Bolognaise, carpaccios, tartars, etc Cocoa and cocoa products Cocoa powders Cocoa-based products and chocolates Raw materials Cocoa powders Chocolates Cocoa beans General remarks and recommendations: Comply with Good Laboratory Practices (GLP; refer to EN ISO 7218 standard and ISO 22174). In the context of NF VALIDATION Certification, samples of more than 25 grams have not been tested. Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 37

38 C Good laboratory practices for PCR and RT-PCR When preparing samples for PCR or RT-PCR amplification: Wear clean gloves and a clean lab coat (not previously worn while handling amplified products or used during sample preparation). Change gloves whenever you suspect that they are contaminated. Maintain separate areas and dedicated equipment and supplies for: Sample preparation and reaction setup. Amplification and analysis of products. Do not bring amplified products into the reaction setup area. Open and close all sample tubes carefully. Avoid splashing or spraying samples. Keep reactions and components capped as much as possible. Use a positive-displacement pipettor or aerosol-resistant barrier pipette tips. Clean lab benches and equipment periodically with 10% bleach solution or DNAZap Solutions (Cat. no. AM9890). For additional information, refer to ISO (2005). 38 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

39 D Safety WARNING! GENERAL SAFETY. Using this product in a manner not specified in the user documentation may result in personal injury or damage to the instrument or device. Ensure that anyone using this product has received instructions in general safety practices for laboratories and the safety information provided in this document. Before using an instrument or device, read and understand the safety information provided in the user documentation provided by the manufacturer of the instrument or device. Before handling chemicals, read and understand all applicable Safety Data Sheets (SDSs) and use appropriate personal protective equipment (gloves, gowns, eye protection, etc). To obtain SDSs, see the Documentation and Support section in this document. Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 39

40 D Appendix D Safety Chemical safety Chemical safety WARNING! GENERAL CHEMICAL HANDLING. To minimize hazards, ensure laboratory personnel read and practice the general safety guidelines for chemical usage, storage, and waste provided below. Consult the relevant SDS for specific precautions and instructions: Read and understand the Safety Data Sheets (SDSs) provided by the chemical manufacturer before you store, handle, or work with any chemicals or hazardous materials. To obtain SDSs, see the Documentation and Support section in this document. Minimize contact with chemicals. Wear appropriate personal protective equipment when handling chemicals (for example, safety glasses, gloves, or protective clothing). Minimize the inhalation of chemicals. Do not leave chemical containers open. Use only with adequate ventilation (for example, fume hood). Check regularly for chemical leaks or spills. If a leak or spill occurs, follow the manufacturer's cleanup procedures as recommended in the SDS. Handle chemical wastes in a fume hood. Ensure use of primary and secondary waste containers. (A primary waste container holds the immediate waste. A secondary container contains spills or leaks from the primary container. Both containers must be compatible with the waste material and meet federal, state, and local requirements for container storage.) After emptying a waste container, seal it with the cap provided. Characterize (by analysis if necessary) the waste generated by the particular applications, reagents, and substrates used in your laboratory. Ensure that the waste is stored, transferred, transported, and disposed of according to all local, state/provincial, and/or national regulations. IMPORTANT! Radioactive or biohazardous materials may require special handling, and disposal limitations may apply. 40 Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide

41 Appendix D Safety Biological hazard safety D Biological hazard safety WARNING! BIOHAZARD. Biological samples such as tissues, body fluids, infectious agents, and blood of humans and other animals have the potential to transmit infectious diseases. Conduct all work in properly equipped facilities with the appropriate safety equipment (for example, physical containment devices). Safety equipment can also include items for personal protection, such as gloves, coats, gowns, shoe covers, boots, respirators, face shields, safety glasses, or goggles. Individuals should be trained according to applicable regulatory and company/ institution requirements before working with potentially biohazardous materials. Follow all applicable local, state/provincial, and/or national regulations. The following references provide general guidelines when handling biological samples in laboratory environment. U.S. Department of Health and Human Services, Biosafety in Microbiological and Biomedical Laboratories (BMBL), 5th Edition, HHS Publication No. (CDC) , Revised December 2009; found at: World Health Organization, Laboratory Biosafety Manual, 3rd Edition, WHO/CDS/CSR/LYO/ ; found at: Pathatrix Salmonella spp. Kits Linked to MicroSEQ PCR or Selective Agar Detection User Guide 41